[Gate-users] *** Break *** segmentation violation - Gate8
David Boersma
david.boersma at physics.uu.se
Wed Apr 19 11:49:16 CEST 2017
Hi Maikol,
In order to diagnose your problem we need to know not only the output,
but also the input. If you used a macro file, could you please send it
to the list?
If your macro is large and complicated then it would be nice if you
could condense it to a minimal macro that maybe does nothing useful but
still demonstrates this crash in a way that we can reproduce it.
BTW: as far as I know, Gate 8 is not yet released (it's not on the
download page of the opengatecollaboration web site), so I assume that
you work with the develop branch from github. If you got your GATE
source code from somewhere else, then please let us know. It is really
useful to get such reports before the release!
David
Den 13/04/2017 kl. 11:19, skrev maikol salas ramirez:
> Hi all,
>
> I am trying to install Gate-8, but I am facing a problem "/
> **** Break *** segmentation violation*/".
> All the installation process is successful (no error).
>
> I am using Ubuntu 16.04, Root-6.08/00, g++-5.4, gcc-5.4, CLHEP 2.3.1.1,
> Geant4-10.02.03.
>
> I searched on Internet and some people related the problem with ROOT, in
> this case I ran ROOT from binaries and from complete source
> installation, but always is the same, Gate output is:
> /
> **** Break *** segmentation violation
>
>
>
> ===========================================================
> There was a crash.
> This is the entire stack trace of all threads:
> ===========================================================
> #0 0x00007f7995c654ca in __GI___waitpid (pid=2062, stat_loc=stat_loc
> entry=0x7ffddcaf5740, options=options
> entry=0) at ../sysdeps/unix/sysv/linux/waitpid.c:29
> #1 0x00007f7995bdefbb in do_system (line=<optimized out>) at
> ../sysdeps/posix/system.c:148
> #2 0x00007f799c94aab4 in TUnixSystem::Exec (shellcmd=<optimized out>,
> this=0x26c52b0) at
> /home/simu/Programas/Root/root3/root-6.08.00/core/unix/src/TUnixSystem.cxx:2116
> #3 TUnixSystem::StackTrace (this=0x26c52b0) at
> /home/simu/Programas/Root/root3/root-6.08.00/core/unix/src/TUnixSystem.cxx:2403
> #4 0x00007f799c94d40c in TUnixSystem::DispatchSignals (this=0x26c52b0,
> sig=kSigSegmentationViolation) at
> /home/simu/Programas/Root/root3/root-6.08.00/core/unix/src/TUnixSystem.cxx:3661
> #5 <signal handler called>
> #6 G4VelocityTable::Interpolation (this=0x374f1c0) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/track/include/G4VelocityTable.hh:118
> #7 G4VelocityTable::Value (this=0x374f1c0, theEnergy=theEnergy
> entry=-nan(0x8000000000000)) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/track/src/G4VelocityTable.cc:151
> #8 0x00007f799792b230 in G4Track::CalculateVelocity (this=this
> entry=0x3754130) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/track/src/G4Track.cc:247
> #9 0x00007f79979271dc in
> G4ParticleChangeForLoss::UpdateStepForAlongStep (this=0x3584e88,
> pStep=0x319e090) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/track/src/G4ParticleChangeForLoss.cc:230
> #10 0x00007f7999bd2be4 in G4SteppingManager::InvokeAlongStepDoItProcs
> (this=this
> entry=0x319def0) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/tracking/src/G4SteppingManager2.cc:420
> #11 0x00007f7999bd085c in G4SteppingManager::Stepping (this=0x319def0)
> at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/tracking/src/G4SteppingManager.cc:191
> #12 0x00007f7999bdb2e5 in G4TrackingManager::ProcessOneTrack
> (this=0x319deb0, apValueG4Track=apValueG4Track
> entry=0x3754130) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/tracking/src/G4TrackingManager.cc:126
> #13 0x00007f7999e0f5a6 in G4EventManager::DoProcessing (this=0x319de10,
> anEvent=<optimized out>) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/event/src/G4EventManager.cc:184
> #14 0x00007f7999e0fd9c in G4EventManager::ProcessOneEvent
> (this=<optimized out>, anEvent=<optimized out>) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/event/src/G4EventManager.cc:335
> #15 0x00007f799a094657 in G4RunManager::ProcessOneEvent (this=0x2b79ae0,
> i_event=5476) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/run/src/G4RunManager.cc:399
> #16 0x00007f799a092e53 in G4RunManager::DoEventLoop (this=0x2b79ae0,
> n_event=10000, macroFile=<optimized out>, n_select=<optimized out>) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/run/src/G4RunManager.cc:367
> #17 0x00007f799a092b7e in G4RunManager::BeamOn (this=0x2b79ae0,
> n_event=10000, macroFile=0x0, n_select=-1) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/run/src/G4RunManager.cc:273
> #18 0x00000000009ede72 in GateApplicationMgr::StartDAQ() ()
> #19 0x00000000009c9e10 in
> GateApplicationMgrMessenger::SetNewValue(G4UIcommand*, G4String) ()
> #20 0x00007f7996a76a6d in G4UIcommand::DoIt (this=0x350eb20,
> parameterList=...) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/intercoms/src/G4UIcommand.cc:230
> #21 0x00007f7996a8a2dc in G4UImanager::ApplyCommand (this=0x27617d0,
> aCmd=<optimized out>) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/intercoms/src/G4UImanager.cc:523
> #22 0x00007f7996a8a9a8 in G4UImanager::ApplyCommand (this=<optimized
> out>, aCmd=...) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/intercoms/src/G4UImanager.cc:441
> #23 0x00007f7996a67847 in G4UIbatch::ExecCommand (this=this
> entry=0x3514400, command=...) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/intercoms/src/G4UIbatch.cc:170
> #24 0x00007f7996a68a3e in G4UIbatch::SessionStart (this=0x3514400) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/intercoms/src/G4UIbatch.cc:215
> #25 0x00007f7996a8acf2 in G4UImanager::ExecuteMacroFile (this=this
> entry=0x27617d0, fileName=0x7ffddcaf8c90 "mac/main.mac") at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/intercoms/src/G4UImanager.cc:296
> #26 0x00007f7996a7ddd0 in G4UIcontrolMessenger::SetNewValue
> (this=0x2761c00, command=command
> entry=0x2762450, newValue=...) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/intercoms/src/G4UIcontrolMessenger.cc:313
> #27 0x00007f7996a76a6d in G4UIcommand::DoIt (this=0x2762450,
> parameterList=...) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/intercoms/src/G4UIcommand.cc:230
> #28 0x00007f7996a8a2dc in G4UImanager::ApplyCommand (this=0x27617d0,
> aCmd=<optimized out>) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/intercoms/src/G4UImanager.cc:523
> #29 0x00000000004fdb4c in main ()
> ===========================================================
>
>
> The lines below might hint at the cause of the crash.
> You may get help by asking at the ROOT forum http://root.cern.ch/forum.
> Only if you are really convinced it is a bug in ROOT then please submit a
> report at http://root.cern.ch/bugs. Please post the ENTIRE stack trace
> from above as an attachment in addition to anything else
> that might help us fixing this issue.
> ===========================================================
> #6 G4VelocityTable::Interpolation (this=0x374f1c0) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/track/include/G4VelocityTable.hh:118
> #7 G4VelocityTable::Value (this=0x374f1c0, theEnergy=theEnergy
> entry=-nan(0x8000000000000)) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/track/src/G4VelocityTable.cc:151
> #8 0x00007f799792b230 in G4Track::CalculateVelocity (this=this
> entry=0x3754130) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/track/src/G4Track.cc:247
> #9 0x00007f79979271dc in
> G4ParticleChangeForLoss::UpdateStepForAlongStep (this=0x3584e88,
> pStep=0x319e090) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/track/src/G4ParticleChangeForLoss.cc:230
> #10 0x00007f7999bd2be4 in G4SteppingManager::InvokeAlongStepDoItProcs
> (this=this
> entry=0x319def0) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/tracking/src/G4SteppingManager2.cc:420
> #11 0x00007f7999bd085c in G4SteppingManager::Stepping (this=0x319def0)
> at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/tracking/src/G4SteppingManager.cc:191
> #12 0x00007f7999bdb2e5 in G4TrackingManager::ProcessOneTrack
> (this=0x319deb0, apValueG4Track=apValueG4Track
> entry=0x3754130) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/tracking/src/G4TrackingManager.cc:126
> #13 0x00007f7999e0f5a6 in G4EventManager::DoProcessing (this=0x319de10,
> anEvent=<optimized out>) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/event/src/G4EventManager.cc:184
> #14 0x00007f7999e0fd9c in G4EventManager::ProcessOneEvent
> (this=<optimized out>, anEvent=<optimized out>) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/event/src/G4EventManager.cc:335
> #15 0x00007f799a094657 in G4RunManager::ProcessOneEvent (this=0x2b79ae0,
> i_event=5476) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/run/src/G4RunManager.cc:399
> #16 0x00007f799a092e53 in G4RunManager::DoEventLoop (this=0x2b79ae0,
> n_event=10000, macroFile=<optimized out>, n_select=<optimized out>) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/run/src/G4RunManager.cc:367
> #17 0x00007f799a092b7e in G4RunManager::BeamOn (this=0x2b79ae0,
> n_event=10000, macroFile=0x0, n_select=-1) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/run/src/G4RunManager.cc:273
> #18 0x00000000009ede72 in GateApplicationMgr::StartDAQ() ()
> #19 0x00000000009c9e10 in
> GateApplicationMgrMessenger::SetNewValue(G4UIcommand*, G4String) ()
> #20 0x00007f7996a76a6d in G4UIcommand::DoIt (this=0x350eb20,
> parameterList=...) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/intercoms/src/G4UIcommand.cc:230
> #21 0x00007f7996a8a2dc in G4UImanager::ApplyCommand (this=0x27617d0,
> aCmd=<optimized out>) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/intercoms/src/G4UImanager.cc:523
> #22 0x00007f7996a8a9a8 in G4UImanager::ApplyCommand (this=<optimized
> out>, aCmd=...) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/intercoms/src/G4UImanager.cc:441
> #23 0x00007f7996a67847 in G4UIbatch::ExecCommand (this=this
> entry=0x3514400, command=...) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/intercoms/src/G4UIbatch.cc:170
> #24 0x00007f7996a68a3e in G4UIbatch::SessionStart (this=0x3514400) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/intercoms/src/G4UIbatch.cc:215
> #25 0x00007f7996a8acf2 in G4UImanager::ExecuteMacroFile (this=this
> entry=0x27617d0, fileName=0x7ffddcaf8c90 "mac/main.mac") at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/intercoms/src/G4UImanager.cc:296
> #26 0x00007f7996a7ddd0 in G4UIcontrolMessenger::SetNewValue
> (this=0x2761c00, command=command
> entry=0x2762450, newValue=...) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/intercoms/src/G4UIcontrolMessenger.cc:313
> #27 0x00007f7996a76a6d in G4UIcommand::DoIt (this=0x2762450,
> parameterList=...) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/intercoms/src/G4UIcommand.cc:230
> #28 0x00007f7996a8a2dc in G4UImanager::ApplyCommand (this=0x27617d0,
> aCmd=<optimized out>) at
> /home/simu/Programas/Geant4/geant4.10.02.p03/source/intercoms/src/G4UImanager.cc:523
> #29 0x00000000004fdb4c in main ()
> ===========================================================
>
>
> WARNING - Attempt to delete the physical volume store while geometry
> closed !
> WARNING - Attempt to delete the logical volume store while geometry closed !
> WARNING - Attempt to delete the solid store while geometry closed !
> WARNING - Attempt to delete the region store while geometry closed !*/*
> *
>
> The particular is that this error just appear after 1000 or 10000 particles.
>
> If someone knows something, I appreciate any help.
>
> Best Regards
>
>
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